I bisected through recent commits to Rgraphviz and found that 13c8d31 is the first commit that causes the repro I included earlier to fail. 13c8d31 does touch buildEdgeList.c, so at least the basic laws of physics remain intact. But I fail to see how this was a load-bearing call to sprintf.
On Mon, Mar 24, 2025 at 12:04 PM Andrew McDavid <andrew.n.mcda...@gmail.com> wrote: > It works with 2.51.1 and fails with 2.51.5. I haven't tried bisecting > intermediate commits yet. > > On Mon, Mar 24, 2025 at 12:02 PM Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > >> Thanks, super useful. So you're saying it was working with 2.51.1? Or is >> it working with the release version? >> >> Best, >> Kasper >> >> On Mon, Mar 24, 2025 at 12:28 PM Andrew McDavid < >> andrew.n.mcda...@gmail.com> wrote: >> >>> Dear Kasper and Robert, >>>> >>>> b) as I said in my original report, with Rgraphviz 2.51.1, I cannot >>>> reproduce the pEdge error of OncoSimulR in Linux, x86_64 >>> >>> Regarding the "no slot of name "name" for this object of class "pEdge"" >>> error, the interesting thing is that: >>> >>> Dear all, >>> >>> I have been trying to troubleshoot this failure in openCyto and >>> flowWorkspace. I have managed to reproduce it, but there are several >>> things I don't understand. >>> >>> 1) The source version of the package landing page >>> https://bioconductor.org/packages/3.21/bioc/html/Rgraphviz.html (and >>> version that you get with `BiocManager::install`) for Rgraphviz is 2.51.1, >>> but the version being used for the Bioc daily builds is 2.51.5. The >>> binaries for windows and mac have version number 2.51.5. This is deeply >>> mysterious to me. >>> >>> 2) If I manually install the latest version from Kasper's github >>> https://github.com/kasperdanielhansen/Rgraphviz, which is the problematic >>> 2.51.5 version, then I can reproduce the 'no slot of name "name"' error. >>> The error is ultimately in Rgraphviz_buildEdgeList in src/buildEdgeList.c. >>> Below is the most minimal example triggering the error that I've managed to >>> generate so far. It hasn't been very amenable for a unit test, because the >>> source data are from complicated S4 classes. I certainly don't see >>> anything suspicious in the changeset since 2.51.1 that explains the error, >>> but by bisection I guess it did somehow break something in the API that >>> flowWorkspace is using. >>> >>> >>> library(Rgraphviz) >>> aa = list(N_0 = list(edges = 2L), N_2 = list(edges = 3L), N_3 = list( >>> edges = 4L), N_4 = list(edges = c(5L, 6L, 13L)), N_8 = list( >>> edges = integer(0)), N_9 = list(edges = integer(0)), N_13 = list( >>> edges = integer(0)), N_14 = list(edges = integer(0)), N_15 = list( >>> edges = integer(0)), N_16 = list(edges = integer(0)), N_17 = list( >>> edges = integer(0)), N_21 = list(edges = integer(0)), N_22 = list( >>> edges = integer(0))) >>> >>> edgemode_graph = "directed" >>> >>> edgeNames = c("N_0~N_2", "N_2~N_3", "N_3~N_4", "N_4~N_8", "N_4~N_9", >>> "N_4~N_22" >>> ) >>> >>> edgeAttrs = list(lty = c(`N_0~N_2` = "dotted", `N_2~N_3` = "solid", >>> `N_3~N_4` = "solid", >>> `N_4~N_8` = "solid", `N_4~N_9` = "solid", >>> `N_4~N_22` = "solid" >>> )) >>> >>> defAttrs = list(color = "black", dir = "none", weight = "1.0", label = "", >>> fontcolor = "black", arrowhead = "none", arrowtail = "none", >>> fontsize = "14", labelfontsize = "11", arrowsize = "1", >>> headport = "center", >>> layer = "", style = "solid", minlen = "1") >>> >>> >>> .Call("Rgraphviz_buildEdgeList", aa, edgemode_graph, list(), >>> edgeNames, integer(), edgeAttrs, defAttrs, PACKAGE = "Rgraphviz") # >>> i.e. line 45 in R/graphLayout.R >>> >>> >>> >>> >> >> -- >> Best, >> Kasper >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
